Species coexistence in a neutral dynamics with environmental noise

Species coexistence as an emergent effect of interacting mechanisms

Although extensively studied, the maintenance of biodiversity remains a highly debated and investigated topic of contemporary research in ecology. Several studies have quantified the contributions of various coexistence mechanisms to biodiversity. However, often stochastic individual-level interactions are abstracted away, or mechanisms are studied in isolation. The intertwined nature and reciprocal influences between mechanisms, as they arise from individual-level interactions, are therefore rarely considered. We propose a novel mechanistic simulation model grounded in neutral theory to capture and quantify emergent effects arising from such mechanism interactions. Three coexistence mechanisms are supported: storage effect, intransitivity, and resource partitioning. We show that basic neutral dynamics and related models of isolated mechanisms can be replicated. Beyond that, we observe difficult to predict, yet significant emergent effects for mechanism combinations. In some cases, coexistence times could be extended more than tenfold compared to the individual mechanisms' performances. Our findings suggest that studies of individual coexistence mechanisms might be insufficient and indeed misleading for quantifying their overall impact on biodiversity. The particular combination of mechanisms and their interactions appear to be of vital importance.

Population dynamics in a time-varying environment with fat-tailed correlations

Temporal environmental noise (EN) is a prevalent natural phenomenon that controls population and community dynamics, shaping the destiny of biological species and genetic types. Conventional theoretical models often depict EN as a Markovian process with an exponential distribution of correlation times, resulting in two distinct qualitative dynamical categories: quenched (long environmental timescales) and annealed (short environmental timescales). However, numerous empirical studies demonstrate a fat-tailed decay of correlation times. Here we study the consequences of power-law correlated EN on the dynamics of isolated and competing populations. We analyze the intermediate region that lies between the quenched and annealed regimes and show that it can widen indefinitely. Within this region, dynamics is primarily driven by rare, yet not exceedingly rare, long periods of almost-steady environmental conditions. For an isolated population, the time to extinction in this region exhibits a power-law scaling with the logarithm of the abundance and also a nonmonotonic dependence on the spectral exponent.

Processes governing species richness in communities exposed to temporal environmental stochasticity: A review and synthesis of modelling approaches

Research into the processes governing species richness has often assumed that the environment is fixed, whereas realistic environments are often characterised by random fluctuations over time. This temporal environmental stochasticity (TES) changes the demographic rates of species populations, with cascading effects on community dynamics and species richness. Theoretical and applied studies have used process-based mathematical models to determine how TES affects species richness, but under a variety of frameworks. Here, we critically review such studies to synthesise their findings and draw general conclusions. We first provide a broad mathematical framework encompassing the different ways in which TES has been modelled. We then review studies that have analysed models with TES under the assumption of negligible interspecific interactions, such that a community is conceptualised as the sum of independent species populations. These analyses have highlighted how TES can reduce species richness by increasing the frequency at which a species becomes rare and therefore prone to extinction. Next, we review studies that have relaxed the assumption of negligible interspecific interactions. To simplify the corresponding models and make them analytically tractable, such studies have used mean-field theory to derive fixed parameters representing the typical strength of interspecific interactions under TES. The resulting analyses have highlighted community-level effects that determine how TES affects species richness, for species that compete for a common limiting resource. With short temporal correlations of environmental conditions, a non-linear averaging effect of interspecific competition strength over time gives an increase in species richness. In contrast, with long temporal correlations of environmental conditions, strong selection favouring the fittest species between changes in environmental conditions results in a decrease in species richness. We compare such results with those from invasion analysis, which examines invasion growth rates (IGRs) instead of species richness directly. Qualitative differences sometimes arise because the IGR is the expected growth rate of a species when it is rare, which does not capture the variation around this mean or the probability of the species becoming rare. Our review elucidates key processes that have been found to mediate the negative and positive effects of TES on species richness, and by doing so highlights key areas for future research.

Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance

There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behaviour leading to the coexistence of resistant and sensitive cells in large populations and static environments. This picture is, however, greatly altered by the fluctuations arising in volatile environments, in which microbial communities commonly evolve. Here, we study the eco-evolutionary dynamics of a population consisting of an antimicrobial-resistant strain and microbes sensitive to antimicrobial drugs in a time-fluctuating environment, modelled by a carrying capacity randomly switching between states of abundance and scarcity. We assume that antimicrobial resistance (AMR) is a shared public good when the number of resistant cells exceeds a certain threshold. Eco-evolutionary dynamics is thus characterised by demographic noise (birth and death events) coupled to environmental fluctuations which can cause population bottlenecks. By combining analytical and computational means, we determine the environmental conditions for the long-lived coexistence and fixation of both strains, and characterise a fluctuation-driven AMR eradication mechanism, where resistant microbes experience bottlenecks leading to extinction. We also discuss the possible applications of our findings to laboratory-controlled experiments.

Lost in translation? - Caveat to the application of the voter model in ecology and evolutionary biology

The voter model is a paradigmatic model of competition between alternative states within groups. Its properties have been intensively studied in statistical physics. Due to its generality, the model lends itself to various applications in ecology and evolutionary biology. I briefly review these opportunities, but call attention to a frequently occurring misinterpretation: it is often assumed that the agents in the model represent individual organisms. I argue that this assumption only holds under very specific conditions, and thus the meaning of the agents is often 'lost in translation' between physics and biology. Instead of an individual-based view, I propose that an alternative, site-based approach is more plausible. I suggest that the biological applicability of the model could further be broadened by considering the transitional states of the agents (sites) explicitly and letting the network evolve according to the agents' states.

Effect of compositional fluctuation on the survival of bet-hedging species

Understanding the coexistence of diverse species in a changing environment is an important problem in community ecology. Bet-hedging is a strategy that helps species survive in such changing environments. However, studies of bet-hedging have often focused on the expected long-term growth rate of the species by itself, neglecting competition with other coexisting species. Here we study the extinction risk of a bet-hedging species in competition with others. We show that there are three contributions to the extinction risk. The first is the usual demographic fluctuation due to stochastic reproduction and selection processes in finite populations. The second, due to the fluctuation of population growth rate caused by environmental changes, may actually reduce the extinction risk for small populations. Besides those two, we reveal a third contribution, which is unique to bet-hedging species that diversify into multiple phenotypes: The phenotype composition of the population will fluctuate over time, resulting in increased extinction risk. We compare such compositional fluctuation to the demographic and environmental contributions, showing how they have different effects on the extinction risk depending on the population size, generation overlap, and environmental correlation.

Evolution in fluctuating environments: A generic modular approach

Evolutionary processes take place in fluctuating environments, where carrying capacities and selective forces vary over time. The fate of a mutant type and the persistence time of polymorphic states were studied in some specific cases of varying environments, but a generic methodology is still lacking. Here, we present such a general analytic framework. We first identify a set of elementary building blocks, a few basic demographic processes like logistic or exponential growth, competition at equilibrium, sudden decline, and so on. For each of these elementary blocks, we evaluate the mean and the variance of the changes in the frequency of the mutant population. Finally, we show how to find the relevant terms of the diffusion equation for each arbitrary combination of these blocks. Armed with this technique one may calculate easily the quantities that govern the evolutionary dynamics, like the chance of ultimate fixation, the time to absorption, and the time to fixation.

How the storage effect and the number of temporal niches affect biodiversity in stochastic and seasonal environments

Temporal environmental variations affect diversity in communities of competing populations. In particular, the covariance between competition and environment is known to facilitate invasions of rare species via the storage effect. Here we present a quantitative study of the effects of temporal variations in two-species and in diverse communities. Four scenarios are compared: environmental variations may be either periodic (seasonal) or stochastic, and the dynamics may support the storage effect (global competition) or not (local competition). In two-species communities, coexistence is quantified via the mean time to absorption, and we show that stochastic variations yield shorter persistence time because they allow for rare sequences of bad years. In diverse communities, where the steady-state reflects a colonization-extinction equilibrium, the actual number of temporal niches is shown to play a crucial role. When this number is large, the same trends hold: storage effect and periodic variations increase both species richness and the evenness of the community. Surprisingly, when the number of temporal niches is small global competition acts to decrease species richness and evenness, as it focuses the competition to specific periods, thus increasing the effective fitness differences.

One of the major challenges of community ecology and population genetics is the understanding of the factors that protect biodiversity. Surprisingly, in many generic cases temporal environmental variations (and the abundance fluctuations associated with it) promote the coexistence of competing species and facilitate genetic polymorphism. Here we present a detailed and quantitative comparison between the stabilizing (and the destabilizing) effects of periodic (seasonal) and stochastic temporal variations. When the number of species is small, we show that persistence times under periodic variations are much longer than the persistence times in a stochastic environment. However, environmental variations facilitate coexistence only when the number of temporal niches is larger than the number of species, whereas in the opposite case the same mechanism acts to increase competition and to decrease species richness. Since it is reasonable to expect the number of temporal niches under seasonal variations to be typically smaller than the corresponding number in stochastic environments, stochastic variations provide a more plausible explanation for the apparent stability of high-diversity assemblages.

Taming the diffusion approximation through a controlling-factor WKB method

The diffusion approximation (DA) is widely used in the analysis of stochastic population dynamics, from population genetics to ecology and evolution. The DA is an uncontrolled approximation that assumes the smoothness of the calculated quantity over the relevant state space and fails when this property is not satisfied. This failure becomes severe in situations where the direction of selection switches sign. Here we employ the WKB (Wentzel-Kramers-Brillouin) large-deviations method, which requires only the logarithm of a given quantity to be smooth over its state space. Combining the WKB scheme with asymptotic matching techniques, we show how to derive the diffusion approximation in a controlled manner and how to produce better approximations, applicable for much wider regimes of parameters. We also introduce a scalable (independent of population size) WKB-based numerical technique. The method is applied to a central problem in population genetics and evolution, finding the chance of ultimate fixation in a zero-sum, two-types competition.

Intraspecific variability in fluctuating environments: mechanisms of impact on species diversity

Recent studies have found considerable trait variations within species. The effect of such intraspecific trait variability (ITV) on the stability, coexistence, and diversity of ecological communities received considerable attention and in many models it was shown to impede coexistence and decrease species diversity. Here we present a numerical study of the effect of genetically inherited ITV on species persistence and diversity in a temporally fluctuating environment. Two mechanisms are identified. First, ITV buffers populations against varying environmental conditions (portfolio effect) and reduces variation in abundances. Second, the interplay between ITV and environmental variations tends to increase the mean fitness of diverse populations. The first mechanism promotes persistence and tends to increase species richness, while the second reduces the chance of a rare species population (which is usually homogeneous) to invade, thus decreasing species richness. We show that for large communities the portfolio effect is dominant, leading to ITV promoting species persistence and richness.

Population Dynamics in a Changing Environment: Random versus Periodic Switching

Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment modeled by a carrying capacity switching either randomly or periodically between states of abundance and scarcity. The population dynamics is characterized by demographic noise (birth and death events) coupled to a varying environment. We elucidate the similarities and differences of the evolution subject to a stochastically and periodically varying environment. Importantly, the population size distribution is generally found to be broader under intermediate and fast random switching than under periodic variations, which results in markedly different asymptotic behaviors between the fixation probability of random and periodic switching. We also determine the detailed conditions under which the fixation probability of the slow strain is maximal.

Neutral competition in a deterministically changing environment: Revisiting continuum approaches

Environmental variation can play an important role in ecological competition by influencing the relative advantage between competing species. Here, we consider such effects by extending a classical, competitive Moran model to incorporate an environment that fluctuates periodically in time. We adapt methods from work on these classical models to investigate the effects of the magnitude and frequency of environmental fluctuations on two important population statistics: the probability of fixation and the mean time to fixation. In particular, we find that for small frequencies, the system behaves similar to a system with a constant fitness difference between the two species, and for large frequencies, the system behaves similar to a neutrally competitive model. Most interestingly, the system exhibits nontrivial behavior for intermediate frequencies. We conclude by showing that our results agree quite well with recent theoretical work on competitive models with a stochastically changing environment, and discuss how the methods we develop ease the mathematical analysis required to study such models.

Neutral and niche forces as drivers of species selection

The evolutionary and ecological processes behind the origin of species are among the most fundamental problems in biology. In fact, many theoretical hypothesis on different type of speciation have been proposed. In particular, models of sympatric speciation leading to the formation of new species without geographical isolation, are based on the niche hypothesis: the diversification of the population is induced by the competition for a limited set of available resources. Interestingly, neutral models of evolution have shown that stochastic forces are sufficient to generate coexistence of different species. In this work, we put forward this dichotomy within the context of species formation, studying how neutral and niche forces contribute to sympatric speciation in a model ecosystem. In particular, we study the evolution of a population of individuals with asexual reproduction whose inherited characters or phenotypes are specified by both niche-based and neutral traits. We analyze the stationary state of the dynamics, and study the distribution of individuals in the whole phenotypic space. We show, both numerically and analytically, that there is a non-trivial coupling between neutral and niche forces induced by stochastic effects in the evolution of the population allowing the formation of clusters, that is, species in the phenotypic space. Remarkably, our framework can be generalized also to sexual reproduction or other type of population dynamics.

Environmental spatial and temporal variability and its role in non-favoured mutant dynamics

Understanding how environmental variability (or randomness) affects evolution is of fundamental importance for biology. The presence of temporal or spatial variability significantly affects the competition dynamics in populations, and gives rise to some counterintuitive observations. In this paper, we consider both birth-death (BD) or death-birth (DB) Moran processes, which are set up on a circular or a complete graph. We investigate spatial and temporal variability affecting division and/or death parameters. Assuming that mutant and wild-type fitness parameters are drawn from an identical distribution, we study mutant fixation probability and timing. We demonstrate that temporal and spatial types of variability possess fundamentally different properties. Under temporal randomness, in a completely mixed system, minority mutants experience (i) higher than neutral fixation probability and a higher mean conditional fixation time, if the division rates are affected by randomness and (ii) lower fixation probability and lower mean conditional fixation time if the death rates are affected. Once spatial restrictions are imposed, however, these effects completely disappear, and mutants in a circular graph experience neutral dynamics, but only for the DB update rule in case (i) and for the BD rule in case (ii) above. In contrast to this, in the case of spatially variable environment, both for BD/DB processes, both for complete/circular graph and both for division/death rates affected, minority mutants experience a higher than neutral probability of fixation. Fixation time, however, is increased by randomness on a circle, while it decreases for complete graphs under random division rates. A basic difference between temporal and spatial kinds of variability is the types of correlations that occur in the system. Under temporal randomness, mutants are spatially correlated with each other (they simply have equal fitness values at a given moment of time; the same holds for wild-types). Under spatial randomness, there are subtler, temporal correlations among mutant and wild-type cells, which manifest themselves by cells of each type 'claiming' better spots for themselves. Applications of this theory include cancer generation and biofilm dynamics.

Comprehensive phase diagram for logistic populations in fluctuating environment

Population dynamics reflects an underlying birth-death process, where the rates associated with different events may depend on external environmental conditions and on the population density. A whole family of simple and popular deterministic models (such as logistic growth) supports a transcritical bifurcation point between an extinction phase and an active phase. Here we provide a comprehensive analysis of the phases of that system, taking into account both the endogenous demographic noise (random birth and death events) and the effect of environmental stochasticity that causes variations in birth and death rates. Three phases are identified: in the inactive phase the mean time to extinction T is independent of the carrying capacity N and scales logarithmically with the initial population size. In the power-law phase T∼N^{q}, and in the exponential phase T∼exp(αN). All three phases and the transitions between them are studied in detail. The breakdown of the continuum approximation is identified inside the power-law phase, and the accompanying changes in decline modes are analyzed. The applicability of the emerging picture to the analysis of ecological time series and to the management of conservation efforts is briefly discussed.

Phase Diagram for Logistic Systems under Bounded Stochasticity

Extinction is the ultimate absorbing state of any stochastic birth-death process; hence, the time to extinction is an important characteristic of any natural population. Here we consider logistic and logisticlike systems under the combined effect of demographic and bounded environmental stochasticity. Three phases are identified: an inactive phase where the mean time to extinction T increases logarithmically with the initial population size, an active phase where T grows exponentially with the carrying capacity N, and a temporal Griffiths phase, with a power-law relationship between T and N. The system supports an exponential phase only when the noise is bounded, in which case the continuum (diffusion) approximation breaks down within the Griffiths phase. This breakdown is associated with a crossover between qualitatively different survival statistics and decline modes. To study the power-law phase we present a new WKB scheme, which is applicable both in the diffusive and in the nondiffusive regime.

Eco-evolutionary dynamics of a population with randomly switching carrying capacity

Environmental variability greatly influences the eco-evolutionary dynamics of a population, i.e. it affects how its size and composition evolve. Here, we study a well-mixed population of finite and fluctuating size whose growth is limited by a randomly switching carrying capacity. This models the environmental fluctuations between states of resources abundance and scarcity. The population consists of two strains, one growing slightly faster than the other, competing under two scenarios: one in which competition is solely for resources, and one in which the slow (cooperating) strain produces a public good (PG) that benefits also the fast (free-riding) strain. We investigate how the coupling of demographic and environmental (external) noise affects the population's eco-evolutionary dynamics. By analytical and computational means, we study the correlations between the population size and its composition, and discuss the social-dilemma-like 'eco-evolutionary game' characterizing the PG production. We determine in what conditions it is best to produce a PG; when cooperating is beneficial but outcompeted by free riding, and when the PG production is detrimental for cooperators. Within a linear noise approximation to populations of varying size, we also accurately analyse the coupled effects of demographic and environmental noise on the size distribution.

Noise-induced stabilization and fixation in fluctuating environment

The dynamics of a two-species community of N competing individuals are considered, with an emphasis on the role of environmental variations that affect coherently the fitness of entire populations. The chance of fixation of a mutant (or invading) population is calculated as a function of its mean relative fitness, the amplitude of fitness variations and their typical duration. We emphasize the distinction between the case of pairwise competition and the case of global competition; in the latter a noise-induced stabilization mechanism yields a higher chance of fixation for a single mutant. This distinction becomes dramatic in the weak selection regime, where the chance of fixation for a single deleterious mutant is an N-independent constant for global competition and decays like (ln N)⁻¹ in the pairwise competition case. A Wentzel-Kramers-Brillouin (WKB) technique yields a general formula for the chance of fixation of a deleterious mutant in the strong selection regime. The possibility of long-term persistence of large [\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathscr{O}}$$\end{document}O(N)] suboptimal (and extinction-prone) populations is discussed, as well as its relevance to stochastic tunneling between fitness peaks.

Theory of time-averaged neutral dynamics with environmental stochasticity

Competition is the main driver of population dynamics, which shapes the genetic composition of populations and the assembly of ecological communities. Neutral models assume that all the individuals are equivalent and that the dynamics is governed by demographic (shot) noise, with a steady state species abundance distribution (SAD) that reflects a mutation-extinction equilibrium. Recently, many empirical and theoretical studies emphasized the importance of environmental variations that affect coherently the relative fitness of entire populations. Here we consider two generic time-averaged neutral models; in both the relative fitness of each species fluctuates independently in time but its mean is zero. The first (model A) describes a system with local competition and linear fitness dependence of the birth-death rates, while in the second (model B) the competition is global and the fitness dependence is nonlinear. Due to this nonlinearity, model B admits a noise-induced stabilization mechanism that facilitates the invasion of new mutants. A self-consistent mean-field approach is used to reduce the multispecies problem to two-species dynamics, and the large-N asymptotics of the emerging set of Fokker-Planck equations is presented and solved. Our analytic expressions are shown to fit the SADs obtained from extensive Monte Carlo simulations and from numerical solutions of the corresponding master equations.

Survival behavior in the cyclic Lotka-Volterra model with a randomly switching reaction rate

We study the influence of a randomly switching reproduction-predation rate on the survival behavior of the nonspatial cyclic Lotka-Volterra model, also known as the zero-sum rock-paper-scissors game, used to metaphorically describe the cyclic competition between three species. In large and finite populations, demographic fluctuations (internal noise) drive two species to extinction in a finite time, while the species with the smallest reproduction-predation rate is the most likely to be the surviving one (law of the weakest). Here we model environmental (external) noise by assuming that the reproduction-predation rate of the strongest species (the fastest to reproduce and predate) in a given static environment randomly switches between two values corresponding to more and less favorable external conditions. We study the joint effect of environmental and demographic noise on the species survival probabilities and on the mean extinction time. In particular, we investigate whether the survival probabilities follow the law of the weakest and analyze their dependence on the external noise intensity and switching rate. Remarkably, when, on average, there is a finite number of switches prior to extinction, the survival probability of the predator of the species whose reaction rate switches typically varies nonmonotonically with the external noise intensity (with optimal survival about a critical noise strength). We also outline the relationship with the case where all reaction rates switch on markedly different time scales.

Evolution of a Fluctuating Population in a Randomly Switching Environment

Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios-one of pure resource competition, and one in which one strain provides a public good-and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population's fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population's growth rate.

Impact of environmental colored noise in single-species population dynamics

Variability on external conditions has important consequences for the dynamics and the organization of biological systems. In many cases, the characteristic timescale of environmental changes as well as their correlations play a fundamental role in the way living systems adapt and respond to it. A proper mathematical approach to understand population dynamics, thus, requires approaches more refined than, e.g., simple white-noise approximations. To shed further light onto this problem, in this paper we propose a unifying framework based on different analytical and numerical tools available to deal with “colored” environmental noise. In particular, we employ a “unified colored noise approximation” to map the original problem into an effective one with white noise, and then we apply a standard path integral approach to gain analytical understanding. For the sake of specificity, we present our approach using as a guideline a variation of the contact process—which can also be seen as a birth-death process of the Malthus-Verhulst class—where the propagation or birth rate varies stochastically in time. Our approach allows us to tackle in a systematic manner some of the relevant questions concerning population dynamics under environmental variability, such as determining the stationary population density, establishing the conditions under which a population may become extinct, and estimating extinction times. We focus on the emerging phase diagram and its possible phase transitions, underlying how these are affected by the presence of environmental noise time-correlations.

The advantage of being slow: The quasi-neutral contact process

According to the competitive exclusion principle, in a finite ecosystem, extinction occurs naturally when two or more species compete for the same resources. An important question that arises is: when coexistence is not possible, which mechanisms confer an advantage to a given species against the other(s)? In general, it is expected that the species with the higher reproductive/death ratio will win the competition, but other mechanisms, such as asymmetry in interspecific competition or unequal diffusion rates, have been found to change this scenario dramatically. In this work, we examine competitive advantage in the context of quasi-neutral population models, including stochastic models with spatial structure as well as macroscopic (mean-field) descriptions. We employ a two-species contact process in which the “biological clock” of one species is a factor of αslower than that of the other species. Our results provide new insights into how stochasticity and competition interact to determine extinction in finite spatial systems. We find that a species with a slower biological clock has an advantage if resources are limited, winning the competition against a species with a faster clock, in relatively small systems. Periodic or stochastic environmental variations also favor the slower species, even in much larger systems.

Stand Structure and Substrate Diversity as Two Major Drivers for Bryophyte Distribution in a Temperate Montane Ecosystem

Elucidating the major drivers of bryophyte distribution is the first step to protecting bryophyte diversity. Topography, forest, substrates (ground, tree trunks, roots, rocks, and rotten wood), and spatial factor, which factors are the major drivers of bryophyte distribution? In this study, 53 plots were set in 400 m² along the elevation gradient in Xiaoqinling, China. All bryophytes in the plots were collected and identified. Regression analysis was used to examine the relationship between bryophyte and substrate diversity. We compared the patterns of overall bryophyte diversity and diversity of bryophytes found on the ground, tree, and rock along elevational gradients. Canonical correspondence analysis was applied to relate species composition to selected environmental variables. The importance of topography, forest, substrates, and spatial factors was determined by variance partitioning. A total of 1378 bryophyte specimens were collected, and 240 species were identified. Bryophyte diversity was closely related to substrate diversity. The overall bryophyte diversity significantly increased with elevation; however, the response varied among ground, tree, and rock bryophytes. Tree diversity and herb layer were considered important environmental factors in determining bryophyte distribution. Species abundance was best explained by stand structure (17%), and species diversity was best explained by stand structure (35%) and substrate (40%). Results directly indicated that substrate diversity can improve bryophyte species diversity. The effects of micro-habitat formed by stand structure and substrate diversity were higher than those of spatial processes and topography factors on bryophyte distribution. This study proved that the determinant factors influencing bryophyte diversity reflect the trends in recent forest management, providing a real opportunity to improve forest biodiversity conservation.